Hybrid vigor among three geographical populations of Megalobrama amblycephala, including Liangzi Lake population (L), Poyang Lake population (P) and Yuni Lake population (Y), was predicted by combination ability and SSR markers. The first generation individuals of 9 complete diallel cross combinations of three populations were measured with total length and body weight. The analysis of combination ability showed that the sire of Yuni population had the largest general combining ability effective value; however, the largest general combining of total length in dam was Poyang population, while that of body weight was Liangzi population. There were high effective combinations among P♂×P♀, L♂×Y♀ and Y♂×Y♀ which had high specific combining ability, so these combinations were suitable as basic selective populations. The results obtained from SSR markers showed that all three populations had high genetic heterogeneity (He, 0.877-0.863), polymorphism information content (PIC, 0.848-0.820) and marker index (MI, 8.959-11.242). Among the three populations, Liangzi population and Yuni population revealed the largest genetic distance, reaching 0.336 2. According to the result, L♂×Y♀ would have the highest hybrid vigor among those combinations.